Files

• Contig FASTA GJJD01.1.fsa_nt
• Read1 FASTQ SRR15058678_1.fastq
• Flagstat hisat2_SRR15058678.sort.flagstat.txt
• Split srs_SRR15058678_split_alignments.txt
• Candidat srs_SRR15058678_candidates.txt

Contig FASTA - Number of sequences	98 794
Contig FASTA - Mean sequence length	827

Reads statistics

Number of reads	10 490 833
Mean coverage	12.92
Min reads length	15
Max reads length	101
Mean reads length	100.59

Reads length distribution

Number of reads	0
Number of lines in the BAM	10 526 093
Number of mapped reads	7 487 218
Percentage of mapped reads	71.37
Number of properly paired reads	0
Percentage of properly paired reads	0
Secondary alignments	35 260
Singletons alignements	0

Split reads

Number of reads overlapping introns	16 752
Mean length of introns	270.64
Junction TC_GG	927
Junction NN_NN	702
Junction CT_GC	405
Junction AT_AC	339
Junction CT_NN	242
Other junctions	4 462
Canonical junction (GT_AG or CT_AC)	9 675

Detected introns

Number	3 191
Min length	20
Max length	5 511
Mean length	223.01
Min depth	1
Max depth	2 376
Mean depth	5.25

Detected introns depth distribution

Filtered detected introns

Number	110
Filtered because of depth (<= 1)	2 776
Filtered because of length (>= 80%)	52
Filtered because of non canonical junction	1 889
Filtered because of overlapping introns	0
Min length	21
Max length	2 883
Mean length	392.21
Min depth	2
Max depth	2 376
Mean depth	46.5

Top 10 of contigs with the highest number of detected introns

GJJD01002985.1	2 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01085655.1	2 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01000026.1	1 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01000401.1	1 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01000437.1	1 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01000474.1	1 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01000541.1	1 PASS; 2 DP; 0 IO; 0 SS; 0 LEN
GJJD01002305.1	1 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01002766.1	1 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01003126.1	1 PASS; 0 DP; 0 IO; 0 SS; 0 LEN

This glossary reflects terms used in this report:
Candidat : Detected/predicted introns filtrered by canonical junction, length and depth.
Canonic junction: GT_AG or CT_AC for donor and acceptor sites.
Contig : A set of overlapping DNA segments that together represent a consensus region of DNA (source :Wikipedia)
Exon : Coding part of DNA that is translated into protein.
Features : A sequenced chain of nucleic acids which provide protein(s). (source:https://biologydictionary.net/gene/)
Fragment : During sequencing, the fragment is a link between fowarded and reverse reads.
Intron : Any nucleotide sequence removed by RNA splicing during maturation of RNA. (source : Wikipedia)
Reads : An inferred sequence of base pairs corresponding to all or part of a single DNA fragment. (source : Wikipedia)
Sequence : Base pair probabilities of a DNA fragment.
Splice events : a process where exons may be included within or excluded from the final mRNA.
Trimmed contig : Contig without retained intron(s).